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- PDB-6v73: Crystal Structure of Metallo Beta Lactamase from Erythrobacter li... -

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Basic information

Entry
Database: PDB / ID: 6v73
TitleCrystal Structure of Metallo Beta Lactamase from Erythrobacter litoralis with beta mercaptoethanol in the active site
ComponentsBeta-lactamase II
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / FORMIC ACID / Beta-lactamase II
Similarity search - Component
Biological speciesErythrobacter litoralis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMaltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: Crystal Structure of Metallo Beta Lactamase from Erythrobacter litoralis with beta mercaptoethanol in the active site
Authors: Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2476
Polymers25,9571
Non-polymers2905
Water43224
1
A: Beta-lactamase II
hetero molecules

A: Beta-lactamase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,49512
Polymers51,9142
Non-polymers58110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)121.139, 121.139, 90.551
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-305-

FMT

21A-403-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase II


Mass: 25956.982 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Erythrobacter litoralis (strain HTCC2594) (bacteria)
References: UniProt: Q2N9N3

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Non-polymers , 5 types, 29 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3.5M Sodium formate; 0.1M TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 15857 / % possible obs: 99.6 % / Redundancy: 15.1 % / Biso Wilson estimate: 56.42 Å2 / Rsym value: 0.124 / Net I/σ(I): 24.5
Reflection shellResolution: 2.4→2.44 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 735 / CC1/2: 0.527 / Rsym value: 1.052

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V72

6v72


Resolution: 2.4→39.65 Å / SU ML: 0.276 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4066
RfactorNum. reflection% reflection
Rfree0.2406 791 5 %
Rwork0.18 --
obs0.183 15816 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.75 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 10 24 1732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681773
X-RAY DIFFRACTIONf_angle_d0.8182420
X-RAY DIFFRACTIONf_chiral_restr0.0529271
X-RAY DIFFRACTIONf_plane_restr0.0052322
X-RAY DIFFRACTIONf_dihedral_angle_d26.41248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.32961220.2652387X-RAY DIFFRACTION97.44
2.55-2.740.2981370.24282460X-RAY DIFFRACTION99.96
2.74-3.020.31531240.23322486X-RAY DIFFRACTION100
3.02-3.460.24461520.20252468X-RAY DIFFRACTION100
3.46-4.350.19041290.15292536X-RAY DIFFRACTION100
4.35-39.650.23321270.15692688X-RAY DIFFRACTION99.51
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.29273715939-3.7633636968-1.38313388583.020056273693.32691101888.441602245130.06681700015210.3304892039830.4238167799180.05158972172140.08359552375-0.856469662638-0.8939906765060.734255176683-0.07075268086240.500185338178-0.0678530228335-0.008299428489740.5492767940260.1672185090470.652739180407-17.862017568-23.5053486874-21.6827727118
22.38524447438-0.234100726738-0.3078663543843.545443870741.158954221785.05358320202-0.09270580639430.2040096967710.240609019476-0.1282067095960.0428195503169-0.167706683986-0.388560137757-0.1366350016090.05130381071170.329447106422-0.000667178474621-0.05110823688590.3853062523050.1181963696740.367863415544-27.1322708194-29.9830253446-18.706859636
36.87620558145-2.98007010201-6.138726386467.857172901956.362309527867.6176242406-0.2701674548970.252127395495-0.03266365962830.0073379458201-0.1667786753140.02413983478910.433006180763-0.2990742280090.3779167665210.369278854249-0.0302364285507-0.0526939938710.4912664768220.04889528348120.332824403167-31.1314771836-45.472124507-19.7983871009
46.21096524892-1.257070376865.806306052164.70938821819-1.090645407276.17473262780.1160055486190.351297224876-0.193288757755-0.19262431152-0.0806656443257-0.3014642902150.380743081317-0.108208825911-0.1983958189260.3750516435060.006501757853450.03529427432320.5062888996180.0142642324730.525181378555-23.044189544-45.5654441196-23.1653925729
52.319521077760.925823820519-0.9742757856623.894867641840.8083095381714.55763677992-0.0824832998977-0.0554985965056-0.2006665491060.259659726970.101845933414-0.9005338985760.3497086823080.9712408697010.05151942657250.3864495880910.10891621486-0.1241198934240.6381300584750.02727842689950.660728906334-11.37487541-42.9929753165-15.2950288442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 186 )
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 261 )

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